mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 83,587 | A→C | 5.7% | intergenic (‑58/+35) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 83,590 | G→T | 5.3% | intergenic (‑61/+32) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 915,080 | G→C | 6.1% | intergenic (‑223/+272) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 915,081 | G→C | 5.8% | intergenic (‑224/+271) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 940,754 | G→A | 5.0% | intergenic (+34/‑205) | serS → / → dmsA | seryl‑tRNA synthetase/dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 1,041,937 | T→G | 5.2% | intergenic (+22/+93) | appA → / ← etk | phosphoanhydride phosphorylase/tyrosine‑protein kinase, role in O‑antigen capsule formation |
| RA | 1,449,050 | T→A | 5.5% | intergenic (+32/+26) | feaB → / ← tynA | phenylacetaldehyde dehydrogenase/tyramine oxidase, copper‑requiring |
| RA | 1,685,527 | A→G | 100% | G354G (GGT→GGC) | fumC ← | fumarate hydratase (fumarase C),aerobic Class II |
| RA | 1,703,251 | A→T | 5.6% | intergenic (+17/+17) | add → / ← ydgJ | adenosine deaminase/putative oxidoreductase |
| RA | 1,703,252 | A→T | 5.4% | intergenic (+18/+16) | add → / ← ydgJ | adenosine deaminase/putative oxidoreductase |
| RA | 1,865,682 | G→C | 5.6% | intergenic (‑46/+44) | yeaE ← / ← mipA | aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent/scaffolding protein for murein synthesizing machinery |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,985,112 | C→G | 6.9% | intergenic (‑43/+27) | araG ← / ← araF | L‑arabinose ABC transporter ATPase/L‑arabinose ABC transporter periplasmic binding protein |
| RA | 2,145,313 | C→A | 100% | S683Y (TCC→TAC) | yegE → | putative diguanylate cyclase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,286,311 | C→G | 5.6% | intergenic (+24/+79) | proL → / ← yejO | tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| RA | 2,286,313 | T→A | 5.6% | intergenic (+26/+77) | proL → / ← yejO | tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| RA | 2,286,315 | C→G | 5.4% | intergenic (+28/+75) | proL → / ← yejO | tRNA‑Pro/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| RA | 2,305,085 | A→G | 7.7% | intergenic (+692/+23) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,086 | C→G | 7.6% | intergenic (+693/+22) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,087 | C→T | 7.7% | intergenic (+694/+21) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,318,095 | C→G | 100% | L594F (TTG→TTC) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,535,948 | G→C | 100% | D39H (GAT→CAT) | crr → | glucose‑specific enzyme IIA component of PTS |
| RA | 2,906,608 | G→C | 6.4% | intergenic (+25/+35) | ygcG → / ← eno | TPM domain protein, putative phosphatase/enolase |
| RA | 3,171,852 | C→T | 5.1% | intergenic (+19/+27) | qseC → / ← ygiZ | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein |
| RA | 3,239,609 | T→G | 5.7% | intergenic (+64/‑335) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,439,588 | G→C | 7.6% | intergenic (‑79/+28) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,439,589 | G→C | 7.2% | intergenic (‑80/+27) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,739,698 | T→C | 5.5% | intergenic (+171/‑7) | malS → / → avtA | alpha‑amylase/valine‑pyruvate aminotransferase; transaminase C; alanine‑valine transaminase |
| RA | 3,739,717 | C→T | 7.0% | L5F (CTT→TTT) | avtA → | valine‑pyruvate aminotransferase; transaminase C; alanine‑valine transaminase |
| RA | 3,891,502 | C→G | 6.4% | intergenic (+19/‑113) | tnaB → / → mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| RA | 3,891,504 | T→A | 6.4% | intergenic (+21/‑111) | tnaB → / → mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| RA | 3,891,506 | C→G | 6.0% | intergenic (+23/‑109) | tnaB → / → mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| RA | 4,115,901 | G→A | 100% | A441V (GCA→GTA) | glpK ← | glycerol kinase |
| RA | 4,296,060 | C→T | 25.8% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423731–3424234 | 3424562–3424238 | 5–832 | 154 [151] | [146] 153 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 16653 | NA (NA) | 4 (0.020) | 4/254 | NT | NA | noncoding (1267/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 16691 | NA (NA) | noncoding (1305/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | 228359 = | NA (NA) | 3 (0.010) | 3/256 | NT | NA | noncoding (2601/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 228397 = | NA (NA) | noncoding (2639/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 6 (0.020) | 4/250 | NT | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 381823 | NA (NA) | 3 (0.010) | 3/258 | NT | NA | noncoding (564/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381866 | NA (NA) | noncoding (607/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 430968 = | NA (NA) | 7 (0.030) | 4/254 | NT | NA | noncoding (1/98 nt) | REP37 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP37 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | 430993 = | NA (NA) | noncoding (26/98 nt) | REP37 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP37 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | = 984461 | NA (NA) | 7 (0.030) +TAAC |
7/260 | NT | NA | intergenic (+164/+58) | ycbL/aspC | putative metal‑binding enzyme/aspartate aminotransferase, PLP‑dependent |
| ? | NC_000913 | 3774201 = | NA (NA) | intergenic (+7/‑223) | mtlA/mtlD | mannitol‑specific PTS enzyme: IIA, IIB and IIC components/mannitol‑1‑phosphate dehydrogenase, NAD‑dependent | |||||
| * | ? | NC_000913 | 1207790 = | 95 (0.340) | 169 (0.680) | 97/236 | NT | 65.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 94 (0.380) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 98 (0.350) | 155 (0.630) | 101/236 | NT | 63.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 94 (0.380) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 309 (1.140) | 148/260 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 2728214 = | NA (NA) | 9 (0.030) | 5/260 | NT | NA | noncoding (971/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| ? | NC_000913 | 2728240 = | NA (NA) | noncoding (945/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | 2729475 = | 134 (0.480) | 6 (0.020) | 3/248 | NT | 5.5% | intergenic (‑31/+141) | gltW/rrsG | tRNA‑Glu/16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | = 4168363 | 84 (0.320) | intergenic (+163/‑9) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu | |||||
| * | ? | NC_000913 | 3721045 = | 326 (1.160) | 773 (2.780) | 210/266 | NT | 71.9% | noncoding (413/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | = 3839774 | 280 (1.010) | coding (220/819 nt) | nlpA | cytoplasmic membrane lipoprotein‑28 | |||||
| * | ? | NC_000913 | 4542682 = | 212 (0.760) | 13 (0.050) | 13/250 | NT | 5.2% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 279 (1.070) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||